DOCSLIB.ORG

Inhibition Studies of Metalloproteins by Means of Electrochemistry and Spectroscopy Anton Nikolaev

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Inhibition Studies of Metalloproteins by Means of Electrochemistry and Spectroscopy Anton Nikolaev Inhibition studies of metalloproteins by means of electrochemistry and spectroscopy Anton Nikolaev To cite this version: Anton Nikolaev. Inhibition studies of metalloproteins by means of electrochemistry and spectroscopy. Other. Université de Strasbourg, 2018. English. NNT : 2018STRAF053. tel-02146028 HAL Id: tel-02146028 https://tel.archives-ouvertes.fr/tel-02146028 Submitted on 3 Jun 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES CHIMIQUE UMR7140, Chimie de la matière complexe THÈSE présentée par : Anton Nikolaev soutenue le : 29 octobre 2018 pour obtenir le grade de : Docteur de l’université de Strasbourg Discipline/ Spécialité : Chimie Etudes d’inhibition de métalloprotéines par électrochimie et spectroscopie Inhibition studies of metalloproteins by means of electrochemistry and spectroscopy THÈSE dirigée par : Pr HELLWIG Petra, Université de Strasbourg, Strasbourg, France RAPPORTEURS : Pr MIOMANDRE Fabien, Ecole normale supérieure de Cachan, Paris, France Dr LOJOU Elisabeth, BIP CNRS AMU, Marseille, France _______________________________________________________________ AUTRES MEMBRES DU JURY : Dr KIEFFER Bruno, Université de Strasbourg, Strasbourg, France 1 Content Content ........................................................................................................................... 2 Acknowledgments .......................................................................................................... 6 Abbreviations and acronyms ......................................................................................... 7 Resumé en francais........................................................................................................ 9 Préface ............................................................................................................................................................... 9 Partie A. Cytochrome bd-oxydase ...................................................................................................................... 9 Partie B. La protéine mitoNEET ...................................................................................................................... 16 List of the communications ......................................................................................... 18 List of the publications ................................................................................................ 18 Preface .......................................................................................................................... 19 Part A. Cytochrome bd-oxidase ................................................................................... 20 Introduction ..................................................................................................................................................... 20 I. The place of complex IV in the respiratory chain ................................................................. 21 1. Bioenergetic membranes ................................................................................................................. 21 2. Components of respiratory chain .................................................................................................... 22 Eukaryotic respiratory chain ................................................................................................ 22 Cytochrome proteins and heme cofactors ............................................................................. 24 Prokaryotic respiratory chains ............................................................................................. 25 ROS ....................................................................................................................................... 25 Quinols .................................................................................................................................. 26 3. Cytochrome bd is a prokaryotic complex IV ................................................................................... 27 Classification of complex IV ................................................................................................. 28 Structure of complex IV......................................................................................................... 29 A-type oxidases ................................................................................................................. 29 B- and C-type oxidases, NORs .......................................................................................... 31 bd-oxidases ....................................................................................................................... 32 Catalytic cycle ....................................................................................................................... 35 aa3-oxidase ........................................................................................................................ 35 bd-oxidase ......................................................................................................................... 37 Function ................................................................................................................................ 38 II. Inhibitors: role in the protein characterisation .................................................................... 39 1. Kinetic parameters of enzyme catalysis .......................................................................................... 39 2. Influence of the inhibitors on enzyme kinetics Inhibitor classification .......................................... 41 3. Inhibition measurements ................................................................................................................. 43 III. bd-oxidase and inhibitors .................................................................................................. 45 IV. Development of electrochemical biosensor for the detection of inhibitors ....................... 49 1. Biosensors ....................................................................................................................................... 49 2 2. Protein film voltammetry ................................................................................................................ 50 Practical aspects ................................................................................................................... 50 Choice of the surface modification ................................................................................... 50 Gold electrode modified with GNPs covered with SAM ................................................... 54 Comparison of immobilised and solubilised complex IV ...................................................... 54 The aims of the project .................................................................................................................................... 56 Results .............................................................................................................................................................. 57 I. Optimisation of the cyt bd immobilisation. ........................................................................... 58 1. Influence of concentration .............................................................................................................. 58 2. Stability of the signal ...................................................................................................................... 59 Influence of the lipids ............................................................................................................ 60 Desorption or loss of the activity? ........................................................................................ 61 Mutual influence of the surface charge of the SAM and lipid type ....................................... 61 Influence of the thiol spacer length ....................................................................................... 63 Detergent variations ............................................................................................................. 64 3. Improvement of the preparation procedure .................................................................................... 65 GNPs deposition ................................................................................................................... 65 Thiol incubation .................................................................................................................... 67 The protein incubation at the surface ................................................................................... 69 4. Control experiments with HQNO .................................................................................................... 69 5. Conclusions..................................................................................................................................... 71 II. The compound examination. ................................................................................................
Load more

Recommended publications
  • Chapter 5 High-Pressure Stopped-Flow Kinetic Studies of Nnos
    Probing the dynamics and conformational landscape of neuronal nitric oxide synthase A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2013 Anna Sobolewska-Stawiarz Contents Contents ...................................................................................................................... 2 List of Figures ............................................................................................................. 6 List of Tables ............................................................................................................ 10 Abstract ..................................................................................................................... 12 Declaration ................................................................................................................ 13 Copyright Statement ................................................................................................ 13 Acknowledgements ................................................................................................... 14 List of Abbreviations ............................................................................................... 15 List of Amino Acids Abbreviations ........................................................................ 17 CHAPTER 1. INTRODUCTION ........................................................................... 18 1.1 Nitric oxide synthase .........................................................................................
    [Show full text]
  • Bacterial Oxidases of the Cytochrome Bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets
    Published in "Antioxidants & Redox Signaling doi: 10.1089/ars.2020.8039, 2020" which should be cited to refer to this work. Bacterial Oxidases of the Cytochrome bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets Vitaliy B. Borisov,1 Sergey A. Siletsky,1 Alessandro Paiardini,2 David Hoogewijs,3 Elena Forte,2 Alessandro Giuffre`,4 and Robert K. Poole5 Abstract Significance: Cytochrome bd is a ubiquinol:oxygen oxidoreductase of many prokaryotic respiratory chains with a unique structure and functional characteristics. Its primary role is to couple the reduction of molecular oxygen, even at submicromolar concentrations, to water with the generation of a proton motive force used for adenosine triphosphate production. Cytochrome bd is found in many bacterial pathogens and, surprisingly, in bacteria for- mally denoted as anaerobes. It endows bacteria with resistance to various stressors and is a potential drug target. Recent Advances: We summarize recent advances in the biochemistry, structure, and physiological functions of cytochrome bd in the light of exciting new three-dimensional structures of the oxidase. The newly discovered roles of cytochrome bd in contributing to bacterial protection against hydrogen peroxide, nitric oxide, perox- ynitrite, and hydrogen sulfide are assessed. Critical Issues: Fundamental questions remain regarding the precise delineation of electron flow within this multihaem oxidase and how the extraordinarily high affinity for oxygen is accomplished, while endowing bacteria with resistance to other small ligands. Future Directions: It is clear that cytochrome bd is unique in its ability to confer resistance to toxic small molecules, a property that is significant for understanding the propensity of pathogens to possess this oxidase.
    [Show full text]
  • Reconstitution of Active Transport in Proteoliposomes Containing Cytochrome O Oxidase and Lac Carrier Protein Purified from Esch
    Proc. Natl Acad. Sci. USA Vol. 80, pp. 4889-4893, August 1983 Biochemistry Reconstitution of active transport in proteoliposomes containing cytochrome o oxidase and lac carrier protein purified from Escherichia coli (chemiosmotic hypothesis/proton electrochemical gradient/carbocyanine/octyl glucoside/detergent dilution) KAZUNOBU MATSUSHITA*, LEKHA PATEL*, ROBERT B. GENNISt, AND H. RONALD KABACK*t *Roche Institute of Molecular Biology, Roche Research Center, Nutley, New Jersey 07110; and tDepartment of Chemistry, University of Illinois, Urbana, Illinois 61801 Communicated by B. L. Horecker, April 29, 1983 ABSTRACT Most active transport across the bacterial cell flux with appropriately directed lactose concentration gra- membrane is driven by a proton electrochemical gradient dients, and accumulate lactose against a concentration gradient (AJAH+, interior negative and alkaline) generated via electron when AOH+ (interior negative or alkaline or both) is imposed transfer through a membrane-bound respiratory chain. This phe- (2-5). Furthermore, the turnover number of purified lac car- nomenon is now reproduced in vitro with proteoliposomes con- rier in proteoliposomes is similar to that observed in right-side- taining only two proteins purified from the membrane of Esch- out membrane vesicles, as is the Km for lactose (1). In addition, erichia coli. An o-type cytochrome oxidase was extracted from a secondary structure model for the lac carrier protein has been membranes of a cytochrome d terminal oxidase mutant with octyl proposed (6), monoclonal antibodies against the purified pro- 8-D-glucopyranoside after sequential treatment with urea and tein have been prepared and characterized (7), and it has been cholate and was purified to homogeneity by ion-exchange chro- the matography.
    [Show full text]
  • Download English-US Transcript (PDF)
    MITOCW | watch?v=56vQ0S2eAjw SPEAKER 1: The following content is provided under a Creative Commons license. Your support will help MIT OpenCourseWare continue to offer high quality educational resources for free. To make a donation or view additional materials from hundreds of MIT courses, visit MIT OpenCourseWare at ocw.mit.edu. PROFESSOR: Today what I want to do within the lexicon is tell you about nature's most spectacularly beautiful cofactors. And these are formed from vitamin B-12, which you find in your vitamin bottle. OK. So what is the structure of vitamin B-12, and why do I say they are spectacularly beautiful? So it's very hard to see, but if you look at the structure of this, where have you seen a molecule this complicated with five membered rings, each of which has a nitrogen in this? You've seen this when you studied hemoglobin, and you think about heme and proto protoporphyrin IX. If you look at the biosynthetic pathway of heme, a branchpoint of that pathway is to make this ring, which is found in adenosylcobalamin and methylcobalamin, which is what we're going to be focusing on today. And this ring is called the corrin ring. So what I want to do is introduce you a little bit to this corrin ring and what's unusual about it compared to protoporphyrin IX that you've seen before. So the vitamin, as in the case of all vitamins that we've talked about over the course of the semester, is not the actual cofactor used in the enzymatic transformation.
    [Show full text]
  • C12) United States Patent (IO) Patent No.: US 9,441,253 B2 San Et Al
    IIIIII IIIIIIII Ill lllll lllll lllll lllll lllll lllll lllll lllll 111111111111111111 US009441253B2 c12) United States Patent (IO) Patent No.: US 9,441,253 B2 San et al. (45) Date of Patent: Sep.13,2016 (54) METABOLIC TRANSISTOR IN BACTERIA 114/13027 (2013.01); C12Y 205/01001 (2013.01); C12Y 205/01032 (2013.01); C12Y (71) Applicant: William Marsh Rice University, 205/01093 (2013.01); C12Y 305/01022 Houston, TX (US) (2013.01); C12Y 305/99002 (2013.01); C12Y 401/01024 (2013.01); C12Y 602/01011 (72) Inventors: Ka-Yiu San, Houston, TX (US); (2013.01); Y02E 50/17 (2013.01); Y02P 20/52 George N. Bennett, Houston, TX (US); (2015.11) Hui Wu, Houston, TX (US) (58) Field of Classification Search CPC .................................. C12P 7/56; C12N 15/70 (73) Assignee: William Marsh Rice University, Houston, TX (US) USPC .................... 435/108, 111, 115, 116, 252.33 See application file for complete search history. ( *) Notice: Subject to any disclaimer, the term ofthis patent is extended or adjusted under 35 (56) References Cited U.S.C. 154(b) by 130 days. U.S. PATENT DOCUMENTS (21) Appl. No.: 14/176,008 2004/0152159 Al 8/2004 Causey (22) Filed: Feb. 7, 2014 OTHER PUBLICATIONS (65) Prior Publication Data Wu et al. Biotechnology and bioengineering, (Aug. 2015) vol. 112, US 2014/0227745 Al Aug. 14, 2014 No. 8, pp. 1720-1726.* Alper H., Miyaoku K., Stephanopoulos G., (2005) Construction of Related U.S. Application Data lycopene overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat. Biotechnol. 23,612-616.
    [Show full text]
  • Design and Fine-Tuning Redox Potentials of Metalloproteins Involved in Electron Transfer in Bioenergetics
    1 Design and Fine-tuning Redox Potentials of Metalloproteins Involved in Electron Transfer in Bioenergetics Parisa Hosseinzadeh and Yi Lu Abstract: 1. Introduction A significant portion of biological processes are involved with providing vital energy sources such as ATP, and controlling the flow of energy through living systems. These bioenergetics processes, the most important of which are photosynthesis and respiration, require electron transfer (ET) between different redox partners. Metalloproteins are one of the most widely used ET centers in biology. They can be classified into three major classes: cupredoxins, which include type 1 copper (T1Cu) proteins and CuA centers [1- 10], cytochromes [10-17], and iron-sulfur (FeS) proteins [10,18-24]. Each class of ET proteins transfer electrons between different redox partners which possess different reduction potentials (E°) (Figure 1). Therefore, the ET centers need to adjust their E° in a way that matches those of their redox partners. No single class of protein can cover the entire range of physiological E°, which is between ~ -1V, at which protons are reduced to H2, and 1V, at which water is oxidized to O2. Cupredoxins usually function at the high end of the E°, while FeS proteins are mostly involved in ET reactions possessing relatively low E° [10]. The E°’s of FeS proteins overlap significantly with those of cytochromes that often have intermediate E° among the three classes of ET proteins. Figure 1. Reduction potential range of metal centers in electron transfer metalloprotein. Adapted from ref. [10] 2 In this review, we first describe the importance of tuning E° of ET centers, including the metalloproteins described above.
    [Show full text]
  • Iron and Chelation in Biochemistry and Medicine: New Approaches to Controlling Iron Metabolism and Treating Related Diseases
    cells Review Iron and Chelation in Biochemistry and Medicine: New Approaches to Controlling Iron Metabolism and Treating Related Diseases George J. Kontoghiorghes * and Christina N. Kontoghiorghe Postgraduate Research Institute of Science, Technology, Environment and Medicine, CY-3021 Limassol, Cyprus * Correspondence: [email protected]; Tel./Fax: +357-2627-2076 Received: 7 May 2020; Accepted: 5 June 2020; Published: 12 June 2020 Abstract: Iron is essential for all living organisms. Many iron-containing proteins and metabolic pathways play a key role in almost all cellular and physiological functions. The diversity of the activity and function of iron and its associated pathologies is based on bond formation with adjacent ligands and the overall structure of the iron complex in proteins or with other biomolecules. The control of the metabolic pathways of iron absorption, utilization, recycling and excretion by iron-containing proteins ensures normal biologic and physiological activity. Abnormalities in iron-containing proteins, iron metabolic pathways and also other associated processes can lead to an array of diseases. These include iron deficiency, which affects more than a quarter of the world’s population; hemoglobinopathies, which are the most common of the genetic disorders and idiopathic hemochromatosis. Iron is the most common catalyst of free radical production and oxidative stress which are implicated in tissue damage in most pathologic conditions, cancer initiation and progression, neurodegeneration and many other diseases. The interaction of iron and iron-containing proteins with dietary and xenobiotic molecules, including drugs, may affect iron metabolic and disease processes. Deferiprone, deferoxamine, deferasirox and other chelating drugs can offer therapeutic solutions for most diseases associated with iron metabolism including iron overload and deficiency, neurodegeneration and cancer, the detoxification of xenobiotic metals and most diseases associated with free radical pathology.
    [Show full text]
  • SCHELVIS CV Profile 2010
    Curriculum vitae: Johannes Schelvis 09/7/2010 PERSONAL INFORMATION Johannes P. M. Schelvis, Associate Professor Montclair State University Department of Chemistry and Biochemistry 1 Normal Avenue Montclair, NJ 07043 EDUCATION B.S., Physics, 1985, Free University, Amsterdam, Netherlands Ph.D., Biophysics, 1995, University of Leiden, Leiden, Netherlands PROFESSIONAL EXPERIENCE Associate Professor Montclair State University September 2007 – present Assistant Professor New York University September 2000 – August 2007 Postdoctoral Researcher Michigan State University March 1995 - August 2000 HONORS AND AWARDS • Institute Fellow, Margaret and Herman Sokol Institute for the Pharmaceutical Life Sciences at Montclair State University, September 2008 - present • Goddard Fellowship, New York University, 2004 • Whitehead Fellowship for Junior Faculty in Biomedical or Biological Sciences, New York University, 2003. GRANTS AWARDED ACTIVE • "Molecular Mechanisms of Photolyase and Cryptochrome" National Science Foundation, MCB-0920013, August 2009 – July 2012 , $419,453 t.c. (PI) • "Binding of ICER to Its Own Promoter as a Mode of Cooperative Regulation" Margaret and Herman Sokol Institute for Pharmaceutical Life Sciences, September 2008 – August 2011 (1-year no cost extension), $100,000 (PI with Dr. Carlos Molina) • "Light-Driven Damage and Repair of DNA", Faculty Scholarship Program, Montclair State University, 2008 – 2012 , 6 TCH (PI) COMPLETED • "Fingerprinting DNA Damage" Margaret and Herman Sokol Faculty/Student Research Grant Program, July 2008
    [Show full text]
  • Distribution of Cytochromes in Bacteria: Relationship to General Physiology DAVID J
    INTERNATIONAL JOURNAL of SYSTEMATIC BACTERIOLOGY Vol. 23, No. 4 October 1973, p. 459-467 Prin ted in U.S.A. Copyright 0 1973 International Association of Microbiological Societies Distribution of Cytochromes in Bacteria: Relationship to General Physiology DAVID J. MEYER' and COLIN W. JONES Department of Biochemistry, The University of Leicester, England A review of cytochrome occurrence in bacteria is presented which gives the taxonomic distribution of cytochromes and which relates this to general physiological characteristics. Data obtained from published research and recent experimental studies on a total of 169 species of bacteria suggested the existence of four major groupings: (i) the aerobic and facultatively anaerobic, heterotrophic gram positives (cytochrome pattern aa3.0. b.c); (ii) the aerobic and facultatively anaerobic, heterotrophic gram negatives (cytochrome pattern either al.d.o.b.c, a1.o.b.c or aa3.o.b.c); (iii) anaerobic and microaerophilic hetero- trophs (cytochrome pattern b sometimes with al /d/o), and (iv) the ch'emo- and photo-autotrophs (cytochrome pattern c plus czl /aa3/o/b). The absence or minor presence of cytochrome c in facultatively anaerobic and anaerobic heterotrophs was confirmed and was also observed in plant and animal pathogens. Cytochrome d was confined in occurrence mainly to a small taxonomic group of organisms characterized by a high degree of adaptability to unstable habitats. This group was considered for further subdivision dependent upon the conditions causing the production of cytochrome d. As part of an investigation into the occur- ilated on organisms in the three major bacterial orders: rence of more than one spectral type of (i) the taxonomic status of the species according to cytochrome oxidase in many bacteria, a survey Bergey 's Manual of Determinative Bacteriology (13) of published data was carried out.
    [Show full text]
  • Generate Metabolic Map Poster
    Authors: Pallavi Subhraveti Ron Caspi Quang Ong Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_900114035Cyc: Amycolatopsis sacchari DSM 44468 Cellular Overview Connections between pathways are omitted for legibility.
    [Show full text]
  • JOURNAL of BACTERIOLOGY VOLUME 169 DECEMBER 1987 NUMBER 12 Samuel Kaplan, Editor in Chief (1992) Kenneth N
    JOURNAL OF BACTERIOLOGY VOLUME 169 DECEMBER 1987 NUMBER 12 Samuel Kaplan, Editor in Chief (1992) Kenneth N. Timmis, Editor (1992) University of Illinois, Urbana Richard M. Losick, Editor (1988) Centre Medical Universitaire, James D. Friesen, Editor (1992) Harvard University, Cambridge, Mass. Geneva, Switzerland University of Toronto, L. Nicholas Ornston, Editor (1992) Graham C. Walker, Editor (1990) Toronto, Canada Yale University, New Haven, Conn. Massachusetts Institute of Stanley C. Holt, Editor (1987) Robert H. Rownd, Editor (1990) Technology, Cambridge, Mass. The University of Texas Health Northwestern Medical School, Robert A. Weisberg, Editor (1990) Science Center, San Antonio Chicago, Ill. National Institute of Child June J. Lascelles, Editor (1989) Health and Human University of California, Los Angeles Development, Bethesda, Md. EDITORIAL BOARD David Apirion (1988) James G. Ferry (1989) Eva R. Kashket (1987) Palmer Rogers (1987) Stuart J. Austin (1987) David Figurski (1987) David E. Kennell (1988) Barry P. Rosen (1989) Frederick M. Ausubel (1989) Timothy J. Foster (1989) Wil N. Konings (1987) Lucia B. Rothman-Denes (1989) Barbara Bachmann (1987) Robert T. Fraley (1988) Jordan Konisky (1987) Rudiger Schmitt (1989) Manfred E. Bayer (1988) David I. Friedman (1989) Dennis J. Kopecko (1987) June R. Scott (1987) Margret H. Bayer (1989) Masamitsu Futai (1988) Viji Krishnapillai (1988) Jane K. Setlow (1987) Claire M. Berg (1989) Robert Gennis (1988) Terry Krulwich (1987) Peter Setlow (1987) Helmut Bertrand (1988) Jane Gibson (1988) Lasse Lindahl (1987) James A. Shapiro (1988) Terry J. Beveridge (1988) Robert D. Goldman (1988) Jack London (1987) Louis A. Sherman (1988) Donald A. Bryant (1988) Susan Gottesman (1989) Sharon Long (1989) Howard A.
    [Show full text]
  • Characterisation, Classification and Conformational Variability Of
    Characterisation, Classification and Conformational Variability of Organic Enzyme Cofactors Julia D. Fischer European Bioinformatics Institute Clare Hall College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 11 April 2011 This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the word limit of 60,000 words. Acknowledgements I would like to thank all the members of the Thornton research group for their constant interest in my work, their continuous willingness to answer my academic questions, and for their company during my time at the EBI. This includes Saumya Kumar, Sergio Martinez Cuesta, Matthias Ziehm, Dr. Daniela Wieser, Dr. Xun Li, Dr. Irene Pa- patheodorou, Dr. Pedro Ballester, Dr. Abdullah Kahraman, Dr. Rafael Najmanovich, Dr. Tjaart de Beer, Dr. Syed Asad Rahman, Dr. Nicholas Furnham, Dr. Roman Laskowski and Dr. Gemma Holli- day. Special thanks to Asad for allowing me to use early development versions of his SMSD software and for help and advice with the KEGG API installation, to Roman for knowing where to find all kinds of data, to Dani for help with R scripts, to Nick for letting me use his E.C. tree program, to Tjaart for python advice and especially to Gemma for her constant advice and feedback on my work in all aspects, in particular the chemistry side. Most importantly, I would like to thank Prof. Janet Thornton for giving me the chance to work on this project, for all the time she spent in meetings with me and reading my work, for sharing her seemingly limitless knowledge and enthusiasm about the fascinating world of enzymes, and for being such an experienced and motivational advisor.
    [Show full text]